Specimen Kits and Collection
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Specimen identification is a critical part of outbreak investigations. Once the causative agent is known through specimen testing, the public health unit and the home can determine the appropriate next steps to mitigate transmission by implementing targeting interventions. Specimen collection kits (stool or NP) can be ordered through Ottawa Public Health using the Facility Specimen Collection Request Form when an outbreak has been declared. For all other testing purposes, please contact your laboratory services company to obtain the required specimen kits.
Stool specimen kit
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The kit The kit contains two sterile containers, a biohazard bag and requisition sheet. Please refer to the table below for details. Kit contains two sterile containers:
Container Number |
Colour of Cap |
Transport Media |
Test Required |
#1 |
White cap |
Empty vial |
Virology |
#2 |
Green cap |
Red transport medium |
Bacteriology
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The requisition Please ensure that all the sections (1, 2, 4 & 5) of the requisition are completed. Any incomplete requestions will result in their rejection at the laboratory. Take special care to ensure that the following sections and fields are filled out:
- Patient information section
- Public health unit outbreak number
- Date stool sample collected
- Date of symptom onset
The collection: Before collecting:
- Verify the expiration dates on the sterile containers. DO NOT use expired kits, they will be rejected by the testing laboratory.
- If blood or mucous is found in the stool, take the sample from this part of the stool.
- Stool specimens that have been in contact with water in the toilet are unable to be accepted due to contamination.
When collecting: *These first two steps are very important – if the label and/or form are missing information, illegible, or filled out incorrectly, the lab will not test the sample. 1. Fill out the label
- Label the sample containers with the individual’s name, date of birth, health card number (if known), and the date and time the stool sample was collected.
2. Complete the requisition
- Complete all of the required sections of the requisition (see the section on requisitions above).
3. Collect the stool sample
- Individuals who are independent: Defecate into a clean container (i.e., disposable plate, adult incontinence product, collector container).
- Individuals who require assistance/are incontinent: Collect the stool sample from the soiled adult incontinence product.
- Using the individual “scoop” attached to each of the caps, transfer the stool into the corresponding sterile containers. Fill the white cap container first.
- Fill to the line indicated on the container. Do not over fill.
- Tighten the caps. Do not use excessive force to tighten the caps as the containers may crack and leak. Samples that have leaked in transit will be rejected.
- Place the containers in the inner pocket of the plastic biohazard bag and seal it.
- Place the general test requisition form in the small outer pocket of the plastic biohazard bag. DO NOT place the form in the inner pocket.
- Place the biohazard bag into the brown paper bag and refrigerate the sample(s) immediately after collection. Stool samples should be placed on the bottom shelf of a fridge and food should not be stored in the same fridge as the stool samples. A cooler with ice or an ice pack can be used if a separate fridge is not available. DO NOT freeze the samples.
- Perform hand hygiene. If hands are visibly soiled, use soap and water.
- Complete the Facility Specimen Collection Request Form or call Ottawa Public Health at 613-580-2424 x 26325 for stool sample pick-up and delivery to the Public Health Laboratory located in Ottawa. Deadline for same day pick-up is 3:30pm. DO NOT send with your regular lab courier.
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Nasopharyngeal specimen kit
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The kit The kit contains a single test tube, a biohazard bag and requisition sheet. Please refer to Public Heath Ontario’s Respiratory Virus Testing page for more information regarding the types of specimen kits available. The requisition Please ensure that all the sections (1 through 9) of the requisition are completed. Any incomplete requestions will lead to their rejection at the laboratory.
- Ordering Clinician
- Patient Information
- Travel History
- Exposure History
- Test(s) Requested
- Specimen Type
- Patient Setting / Type
- COVID-19 Vaccination Status
- Clinical Information
The collection: Before collecting:
- Verify the expiration dates on the sterile containers. DO NOT use expired kits, they will be rejected by the testing laboratory.
When collecting:
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Influenza, Vaccines and Antivirals
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Influenza For information related to influenza symptoms, transmission, and prevention, refer to the OPH Influenza webpage.
Vaccines Long-term care home (LTCH) and retirement home (RH) sectors are critical stakeholders in the response to influenza. Residents of these institutions are particularly vulnerable to severe illness and death from influenza. Efforts to keep influenza out of these institutions such as early detection of cases and vaccinations are vital to infection prevention and control. To order your flu vaccines for this year’s season, please complete the Influenza Vaccine Order Form or follow the instructions on the memo that will be distributed by the OPH Immunization team. The influenza vaccine consent forms must be completed for each resident including those who have a power of attorney (POA). The consent forms will also be shared via memo by the OPH Immunization team. Antivirals There are currently two antiviral drugs that are licensed in Canada for the treatment and prophylaxis of influenza A and B, including oseltamivir (Tamiflu) and zanamivir (Ralenza). When using antivirals for the treatment of influenza, it is important that they are initiated as soon as possible within 48 hours of symptom onset. OPH recommends oseltamivir as the drug of choice for both the treatment and prophylaxis of residents in long-term care homes (LTCHs) for the following reasons:
- The use of Zanamivir has not been proven effective for prophylaxis of influenza in the LTCH setting
- Elderly individuals may have difficulty inhaling zanamivir
- Zanamivir is not recommended for treatment or prophylaxis of influenza in individuals with underlying respiratory conditions such as chronic obstructive pulmonary disease (COPD) or asthma due to the risk of bronchospasms
- Reimbursement for zanamivir for residents occurs only when the predominant strain is resistant to oseltamivir
Flumist is a vaccine option in Ontario that is only publicly funded for children from 2-17 years of age. If a staff member or resident chooses to be immunized with Flumist privately, it is recommended that LAIV (Flumist) not be administered until 48 hours after antiviral treatment or prophylaxis for influenza is stopped.
Management of staff during an Influenza outbreak
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It is important for staff to be advised upon hire about the influenza policy of the facility and/or their collective agreement, and the options available to them in the event of an influenza outbreak if they are not immunized. When an influenza outbreak occurs, staff must obtain prescriptions for antiviral medication from their own health care provider and are responsible for their own antiviral-related expenses, unless they have coverage through a company or private health insurance plan. They are not eligible for prescription drug coverage under any circumstances from the Ontario Drug Program (ODP). Only under very specific circumstances, immunized health care workers may be eligible for reimbursement through the High Intensity Needs Fund (HINF). During a laboratory-confirmed influenza outbreak, when the circulating strain is not well-matched by the vaccine, antiviral prophylaxis should be offered to all staff, regardless of vaccination status, until the outbreak is declared over, based on consultation with OPH. Immunized Staff
Period between immunization and outbreak declaration |
Immunized (inactivated vaccine) |
Immunized (live attenuated vaccine - i.e. Flumist) |
More than 2 weeks |
- No work restrictions
- Prophylaxis if circulating strain is not well-matched by vaccine
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- No work restrictions
- Prophylaxis if circulating strain is not well-matched by vaccine
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Less than 2 weeks |
- Prophylaxis until immunity is reached or outbreak is declared over, whichever is shorter
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- No antiviral prophylaxis or treatment for at least 2 weeks after vaccination (unless medically indicated)
- If antivirals are administered within this time frame, re-vaccinate immediately with inactivated vaccine
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Unimmunized Staff
- Unimmunized staff should be offered vaccine and take antiviral prophylaxis until immunity is reached or until the outbreak is declared over, whichever is shorter.
- Unimmunized staff who refuse to be immunized must take antiviral prophylaxis until the outbreak is declared over; staff may work with residents as soon as they start antiviral prophylaxis.
- Staff accepting to be immunized, but refusing antiviral medication, should NOT be permitted to work in the outbreak-affected area for a two-week period. Prior to being reassigned to another unit, they must be asymptomatic for 72 hours (3 days).
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Management of residents during an Influenza outbreak
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Prophylaxis
- During a laboratory-confirmed influenza outbreak, antiviral prophylaxis should be offered to all residents in the outbreak-affected area who are NOT already ill with influenza, regardless of immunization status, until the outbreak is declared over
- If respiratory symptoms develop in a resident while on prophylaxis, the dose should be switched to a treatment dose for five days. After five days, if influenza is not lab confirmed, the resident should return to the prophylactic dose until the end of the outbreak.
Treatment Once an outbreak has been laboratory-confirmed as influenza, additional laboratory confirmation of new cases is not required to begin treatment of residents who meet case definition. It is important that:
- Antiviral treatment of ill residents who meet case definition is started as soon as possible, and within 48 hours of symptom onset
- Ill residents remain in their rooms for the duration of the antiviral treatment, which should be a total of five days
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Circumstances that may affect decisions regarding use of antiviral medication
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- If the resident meets case definition and has been symptomatic for MORE than 48 hours and antiviral treatment has NOT been started, use Appendix A for making decisions about the use of antivirals.
- If the outbreak is ongoing when the five-day treatment course ends AND the resident did NOT have lab-confirmed influenza (either the resident was never tested or had a negative influenza lab result) but was symptomatic, the resident should be switched to a prophylactic dose until the outbreak is declared over. This is recommended in case of a potential outbreak caused by more than one agent (see Appendix B).
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When antiviral medications do not control the outbreak
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If new cases continue to appear 72 to 96 hours after the start of antivirals, consider the following:
- The new cases could be caused by another organism.
- There could be compliance/adherence issues.
- Resistance to the antiviral medications may have developed in the circulating strain.
In the event that the outbreak is not controlled with antiviral use:
- Consult with the OPH Outbreak Management team to determine if the antiviral agents should be continued.
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Recommended dosage for prophylaxis and treatment of influenza with Tamiflu for adults
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Recommended dosage for prophylaxis and treatment of influenza with Tamiflu for adults
Kidney function/Creatinine clearance |
Prophylaxis is given until the outbreak is declared over |
Treatment for five days |
With no known renal disease OR With renal disease and creatinine clearance >60mL/min |
75 mg once daily |
75 mg twice daily |
With known renal disease and creatinine clearance of >30-60mL/min |
75 mg on alternate days OR 30 mg once daily |
75 mg once daily OR 30 mg suspension twice daily OR 30 mg capsule twice daily |
With known renal disease and creatinine clearance of 10- 30 mL/min |
30 mg every other day |
30 mg orally once daily |
Residents with renal failure (<10 mL/min) |
No data |
Single dose of 75 mg for the duration of the illness |
Dialysis residents: Low-Flux HD |
30 mg orally after every alternate hemodialysis session (initial dose can be started between sessions) |
30 mg orally after every hemodialysis session (initial dose can be started between sessions) |
Dialysis residents: High -Flux HD |
No data |
75 mg after each dialysis session |
Dialysis residents: CAPD dialysis |
30 mg orally once weekly Administered prior to the start of dialysis |
A single dose of 30 mg orally administered prior to the start of dialysis |
Dialysis residents: CRRT high-flux dialysis |
No data |
30 mg daily or 75 mg every second day |
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Appendix A: Influenza Outbreak antiviral treatment recommendations if treatment is not initiated within 48 hours of symptom onset
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Diagram 1: Influenza Outbreak antiviral treatment recommendations if treatment is not initiated within 48 hours of symptom onset
- Resident meets outbreak case definition
- Was antiviral treatment initiated within 48 hours of symptom onset? (NO)
- Is the resident clinically improving?
- NO
Provide antiviral treatment
- YES
Consider antiviral therapy for individuals in high risk groups*, or individuals with moderate, severe or complicated illness
* Note: please see AMMI Influenza guidelines (as current) for a definition of high-risk groups
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Appendix B: Influenza Outbreak antiviral prophylaxis recommendations for Line- listed cases after completion of treatment with antiviral medication
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Diagram 2: Influenza Outbreak antiviral prophylaxis recommendations for Line- listed cases after completion of treatment with antiviral medication  Is the outbreak still ongoing?
- NO
No further action required
- YES
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References |
- Hoffman-La Roche Limited, Tamiflu Product Monograph, Jan 2015
- AMMI Canada Guidelines, Update on Influenza Antiviral Drug Treatment and Prophylaxis for the 2015-2016 Influenza Season, 2016
- AMMI Canada Guidelines, Guidance for Practitioners on the Use of Antiviral Drugs to Control Influenza Outbreaks in Long-Term Care Facilities in Canada, 2014-2015 Season, 2015
- AMMI Canada Guidelines, The Use of Antiviral Drugs for Influenza: A Foundation Document for Practitioners, 2013
- Canadian Immunization Guide, Canadian Immunization Guide Chapter on Influenza and Statement on Seasonal Influenza Vaccine for 2016-2017, 2016
- Ministry of Health and Long-Term Care, A Guide to the Control of Respiratory Infection Outbreaks in Long-Term Care Homes, Nov 2015
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COVID-19 Vaccines and COVaxon |
As part of the current efforts to reach increased coverage targets in the province to protect individuals and the population, it is important to take every opportunity to vaccinate. All LTCH and RHs who have the clinical capacity to immunize are eligible to order COVID-19 vaccine for administration to eligible staff and residents within their facility.
Vaccine Ordering Process
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LTCH and RH operators can order vaccine and vaccination supplies by completing the COVID-19 Vaccine Order Form. OPH will arrange delivery of vaccine on the date indicated on the COVID-19 Vaccine Order Form submitted. Deliveries can only be scheduled Monday through Friday between 8 am to 5 pm. Note: Requests for vaccine must be submitted a minimum of two business days prior to the planned vaccine administration date and are based on vaccine availability.
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LTCH and RH that require immunization support
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OPH encourages all homes to explore leveraging partnerships used for the flu vaccine, to see if they have capacity to support with COVID-19 vaccines as well. For LTCH and RH homes with limited capacity, OPH will continue to offer on-site training for staff and work with the home to collaboratively run a clinic. The training provided will help increase capacity for the home to immunize residents who may require their initial or subsequent booster doses in the future. To request OPH support for a clinic (including staff training):
- Ensure you have completed the COVID-19 Vaccine Consent Form for each resident who has a POA.
- Once above forms are complete, then submit your facility information via the Long Term Care and Retirement Home COVID-19 OPH Clinic and Training Request Form.
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COVaxON requirements and educational resources |
COVaxON is Ontario’s provincial vaccination database for COVID-19 vaccines. All doses of COVID-19 vaccine administered must be documented in the COVaxON system. Please ensure that your facility has active access to COVaxON prior to the day of your vaccination event.
COVaxON Training Support for Ottawa-area Homes
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A COVax SharePoint Site was developed for training purposes and gives COVax users who are registered under OPH’s authorized organization (AO) access to various COVax training materials, including demo session recordings, weekly provincial go-live training schedules, learning modules, job aids, tailored user training roadmaps, system change and so much more. Should you require Training support and access to the SharePoint please contact covaxon@ottawa.ca.
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COVaxON Concierge Service for Ottawa-area Homes
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Additional on-boarding & training assistance is available exclusively to new COVax users. Should you require additional support, please fill out the COVax Concierge Service Request Form and someone from the OPH COVax Support Team will contact you. PLEASE NOTE: This mailbox is monitored Monday- Friday between 8:00 am to 4:00 pm.
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COVaxON Technical Support
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The provincial COVaxON portal will assist with COVaxON Application and User Management support. Contact information is as follows: Phone: (416) 637-8672 or Toll Free 1-888-333-0640. Email: COvaxonsupport@ontario.ca. The support hours are 7:00 am to 8:00 pm, 7 days a week.
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COVID-19 Immunization Information for Immunizers |
Below are links to COVID-19 vaccine-relevant resources for immunizers. These include guidance for health care providers related to administration, special recommendations as well as anaphylaxis and adverse event management. Please visit the Ministry of Health COVID-19 Website for additional information. Pfizer-BioNTech
Moderna COVID-19 Vaccine
Mixed COVID-19 mRNA Vaccine Schedules
Adverse Events
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Storage and Handling of COVID-19 Vaccines |
For information related to the storage and handling of COVID-19 vaccines, please access Storage and Handling of Pfizer-BioNTech’s COVID-19 and/or Storage and Handling of Moderna COVID-19 Vaccines. |
Printed confirmation of vaccination |
Do you have staff or residents that require a printed confirmation of their vaccination status? Individuals can review and print a confirmation that they have received their vaccine through the Ontario COVID-19 Vaccination portal. |
Additional Resources |
COVID-19 Vaccination Recommendations for Special Populations Guidance document from the Ministry of Health outlining currently available scientific knowledge for COVID-19 vaccination in special populations and expert clinician advice.
MOHLTC COVID-19 Vaccine Promotion Toolkit A toolkit to help boost vaccination rates in LTCH and RH. The kit contains a welcome letter, posters, fact sheets, tips for holding effective conversations, an FAQ, and more. The toolkit is available in English, French and 10 other languages. |
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Activities in Long-Term Care Homes and Retirement homes during an outbreak |
It is important for Long-Term Care Homes and Retirement Homes to assess and modify activities during the course of enteric and respiratory outbreaks to reduce the risk of transmission of infection amongst the residents and staff. Each outbreak is unique and the Ottawa Public Health investigator assigned to the outbreak will assist you with outbreak management and activity assessment. Please see Ottawa Public Health’s Activities in Long-term Care Homes and Retirement Homes during Outbreaks webpage for additional information. |
Family and visitor information during and outbreak |
Outbreaks of illness sometimes occur in healthcare facilities and can be a stressful time for families and staff. Outbreaks are most often caused by common viruses that produce symptoms of gastroenteritis, such as nausea, vomiting and diarrhea, or respiratory illness, such as fever, cough, and sore throat. These viruses generally spread from person to person, or by touching contaminated surfaces, objects or equipment and then touching your eyes, mouth, nose or handling food or drink. For the health and well-being of everyone, it is important to implement measures to control the spread of infection as soon as possible. Ways you can help stop the spread of illness:
- Do not visit if you are ill
- Follow the outbreak and infection control measures recommended
- Limit your visit to your family or friend
- If you are visiting and ill family member of friend, please check with the staff prior to entering his or her room
- Wear a mask, if/when applicable
- Clean your hands often with liquid soap and running water or alcohol-based hand sanitizer
- Get immunized against influenza every year
When to wash your hands:
- When entering the facility and before leaving
- Before entering and after leaving a resident’s room
- Before eating or assisting your family member or friend with his or her meals
- After going to the washroom, coughing, or blowing your nose
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Additional guidance from partnering organizations |
To learn more about requirements for long-term care homes and retirement homes with respect to COVID 19, please refer to the following resources:
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